User GuideΒΆ Introduction to FastSurfer Getting started Requirements to input images System Requirements Expert usage FreeSurfer Downstream Modules Intended Use References Acknowledgements Installation Linux MacOS Windows Examples Example 1: FastSurfer Docker Example 2: FastSurfer Singularity Example 3: Native FastSurfer on subjectX with parallel processing of hemis Example 4: FastSurfer on multiple subjects Example 5: Quick Segmentation Example 6: Running FastSurfer on a SLURM cluster via Singularity Flags Required arguments Required for docker when running surface module Segmentation pipeline arguments (optional) Surface pipeline arguments (optional) Other Output files Segmentation module Cerebnet module HypVINN module Surface module Docker Support Pull FastSurfer from DockerHub FastSurfer Docker Image Creation Build docker image with attestation and provenance Singularity Support Singularity with the official FastSurfer Image Building your own FastSurfer Singularity Image FastSurfer Singularity Image Usage Singularity Best Practice Manual Edits Pipeline Possible Edits 1. T1 Pre-Processing: 2. Segmentation Edits 3. Brainmask Edits: Security Policy Supported Versions Reporting a Vulnerability Contributor Covenant Code of Conduct Our Pledge Our Standards Our Responsibilities Scope Enforcement Attribution Contributing to FastSurfer Reporting Bugs Suggesting Enhancements Contributing Code Attribution FastSurfer License Apache License